Cavity programs: Difference between revisions
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*A '''channel''' connects two entrances<ref name="caverweb" />. | *A '''channel''' connects two entrances<ref name="caverweb" />. | ||
*A '''pore''' may mean a trans-membrane channel through an integral membrane protein<ref name="moleonline" /> | *A '''pore''' may mean a trans-membrane channel through an integral membrane protein<ref name="moleonline" /> | ||
*Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="moleonline" /><ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref>. | *Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="moleonline" /><ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref><ref name="avp">The term ''void'' is used for the program [http://www.bioinf.org.uk/software/avp/ AVP (Another Void Program)] from the group of Andrew C. R. Martin at University College, London UK.</ref>. | ||
Nearly all proteins have irregular surfaces with shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a deep pocket can also be termed a tunnel accessing a functional or catalytic site<ref name="damborsky3" /><ref name="kingsley" />. | Nearly all proteins have irregular surfaces with shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a deep pocket can also be termed a tunnel accessing a functional or catalytic site<ref name="damborsky3" /><ref name="kingsley" />. | ||
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===I. Cavities=== | ===I. Cavities=== | ||
These programs identify any cavities between atoms of the macromolecule, or pockets beneath a smoothed macromolecular surface, that are larger than the probe diameter. '''No starting position need be specified'''. | These programs identify any cavities between atoms of the macromolecule, or pockets beneath a smoothed macromolecular surface, that are larger than the probe diameter. '''No starting position need be specified'''. | ||
*[[#AVP|AVP]] | |||
*[[#CASTp|CASTp]] | *[[#CASTp|CASTp]] | ||
*[[#Jmol|Jmol]] Cavities as isosurfaces. | *[[#Jmol|Jmol]] Cavities as isosurfaces. | ||
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*[[#MAP_CHANNELS|MAP_CHANNELS]] for solvent channels in crystals of macromolecules. | *[[#MAP_CHANNELS|MAP_CHANNELS]] for solvent channels in crystals of macromolecules. | ||
</td></tr></table> | </td></tr></table> | ||
==AVP== | |||
[http://www.bioinf.org.uk/software/avp/ AVP (Another Void Program)]: "Voids are defined as | |||
holes in the protein that are not accessible to solvent, but into | |||
which a molecule of a given radius (such as a water) can fit. ... Initially a course grid is used (default 1A), but close to the protein a finer grid (default 0.1A) is | |||
used and off-grid locations are explored." In addition to locating voids, the program assesses packing quality. | |||
(<font color="red">To be continued ...</font>) | |||
==CASTp== | ==CASTp== | ||
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First released December, 2020. | First released December, 2020. | ||
==See Also== | |||
*[[Jmol/Cavities pockets and tunnels]] | |||
*[[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]] | |||
*[[Jmol/Depth from surface]] | |||
*[[SARS-CoV-2 spike protein fusion transformation]] which discusses the spike protein cavity used as an example above. | |||
==References== | ==References== | ||
<references /> | <references /> | ||
